rs4078417

chr14-51290164-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064164.1(LOC124903315):n.633+2101A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,164 control chromosomes in the GnomAD database, including 6,356 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6356 hom., cov: 32)
• Consequence: LOC124903315 XR_007064164.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774

Genes affected

LOC124903315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903315	XR_007064164.1	n.633+2101A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38530 AN: 152046 Hom.: 6352 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.253 AC: 38540 AN: 152164 Hom.: 6356 Cov.: 32 AF XY: 0.251 AC XY: 18694 AN XY: 74384

Gnomad4 AFR AF: 0.0640

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.254

Alfa AF: 0.326 Hom.: 5010

Bravo AF: 0.248

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.4
Dann	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4078417; hg19: chr14-51756882;